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        "author": "Katie Porter",
        "author_email": "kaporter@bu.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: MacOS",
            "Operating System :: POSIX",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "cluspro_api\n===========\n\nPython library and associated scripts for submiting jobs and\ndownloading results from ClusPro.\n\nInstallation\n------------\n\nEnsure you have ``pip``, then run:\n\n.. code-block:: bash\n\n    pip install --user cluspro_api\n\nor\n\n.. code-block:: bash\n\n   [sudo] pip install cluspro_api\n\n``sudo`` is only needed if you are installing globally. If ``--user`` option is used, binaries\nwill be in ``$HOME/.local/bin``. We recommend use of Anaconda (https://www.continuum.io). \n\nUsage\n-----\n\nSubmitting Jobs\n~~~~~~~~~~~~~~~\n\nTo submit a docking job to ClusPro:\n\n.. code-block:: bash\n\n    cluspro_submit --receptor <path to receptor pdb file> --ligand <path to ligand pdb file>\n\nThis will prompt you for your username and API secret, which can be found on the API tab\nafter logging into ClusPro. These will be stored in a ``.clusprorc`` file in your home\ndirectory.\n\nOptions: \n\n.. code-block:: bash\n\n    $ cluspro_submit --help\n\n    Usage: cluspro_submit [OPTIONS]\n\n     Jobs are expected to be in one of four \"modes\": docking with a provided\n     ligand PDB ID or PDB file, docking in multimer mode (using --multimer), or\n     peptide docking (using --pepmot and --pepseq). If using multimer mode add\n     --multimer and specify dimer or trimer (ex. --multimer dimer or --multimer\n     trimer). If using peptide mode supply both the peptide motif and sequence\n     (ex. --pepmot KXRRL --pepseq KGRRL). If using dimer classification mode add\n     --dcmode and provide the chain(s) that define the potential dimer interface\n     (ex. --rec-chains and --lig-chains). Mixing options from these four modes\n     is not supported and will result in an error message.\n\n    Options:\n      --username TEXT\n      --secret TEXT\n      --coeffs PATH               Coefficients file [Advanced]\n      --rotations PATH            Rotations file [Advanced]\n      -j, --jobname TEXT          Will default to job number\n      -a, --antibodymode          Use Antibody mode [Advanced]\n      -o, --othersmode            Use Others mode [Advanced]\n      --receptor PATH             Upload a PDB file\n      --ligand PATH               Upload a PDB file\n      --recpdb TEXT               4-letter PDB code\n      --ligpdb TEXT               4-letter PDB code\n      --pepmot TEXT               Peptide motif\n      --pepseq TEXT               Peptide sequence\n      --pepexclusion TEXT         List of PDB ids to exclude from motif\n                                  search\n      --rec-chains TEXT           Chains to use, for example \"A B\" (in double\n                                  quotes)\n      --lig-chains TEXT           Chains to use, for example \"A B\" (in double\n                                  quotes)\n      --rec-mask PATH             Receptor mask [Advanced]\n      --lig-mask PATH             Ligand mask [Advanced]\n      --rec-attraction PATH       Receptor attraction [Advanced]\n      --lig-attraction PATH       Ligand attraction [Advanced]\n      --rec-dssp                  Remove unstructured terminal residues in\n                                  receptor [Advanced]\n      --lig-dssp                  Remove unstructured terminal residues in ligand [Advanced]\n      --restraints PATH           Upload restraints file [Advanced]\n      --saxs-file PATH            Upload SAXS profile [Advanced]\n      --masknoncdr                Automatically mask non-CDR region, Antibody mode only [Advanced]\n      --multimers [dimer|trimer]  Multimer mode [Advanced]\n      --dcmode                    Use Dimer Classification mode\n      --help                      Show this message and exit\n\nIf you write a script which submits the jobs in a loop, please submit no more than 50 jobs\nper batch (and then wait until these jobs finish before submitting more). Please pause for\n5-10 seconds between job submissions within each batch. \n\nRunning ``cluspro_submit`` will print out the cluspro job id, which you should record and use\nlater to download your job results. \n\nDownloading Results\n~~~~~~~~~~~~~~~~~~~\n\nTo download results from a finished job:\n\n.. code-block:: bash\n\n    cluspro_download <jobid>\n\nYou can download multiple jobs at once:\n\n.. code-block:: bash\n\n    cluspro_download <jobid1> <jobid2> <jobid3> ...\n\nThe results will be saved in the directory from which you ran the command.",
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